I am having the same problem. We upgraded our site from CMS 5 R2 > 6 > 6 R2. After upgrading, our master (default) languages is "en". All the other languages will display in the url, but the default language will not have "en" in the url. This causes big problems for us. Is there a solution to this? It never worked this way in CMS 5. I am assuming it may be a bug?

Yes, I think we changed this behavior going from 5 R2 Sp2 to 6 R1. You could solve it by doing a redirect in IIS. So if you go to www.site.com you get to redirected to www.site.com/en/ or what ever language you have as default.

Also, check your EPiServerFramework.config and see if you have a set a language for a address/url or not. If you have, then it will strip away the language code from the urls. 

It was set in my EPiServerFramework.congif to have <add name="*" language="en" />, so I removed the language="en" part and it is now <add name="*" />  but will this cause any problems anywhere else for users coming from other countries? I tested it out and it seems to all be ok. Not sure if it's something that's not obvious that it could affect.

If not, it's all set. Thanks!

I think you should read  http://world.episerver.com/Documentation/Items/Tech-Notes/EPiServer-CMS-6/EPiServer-CMS-6-R2/Globalization/to get a better sense of what is happening behind the scenes.

But short answer is no, shouldn't make a difference if you have set up English as the default language in web.config.